post graduate diploma in bioinformatics (p.g.d.b.i) · languages – basics of c programming,...
TRANSCRIPT
Post Graduate Diploma in Bioinformatics (P.G.D.B.I)
SEM Course Code Course Course Title Hrs /
Week Credit
CIA
Mark
SE
Mark
Total
Marks
I
20PDBI1C1 Core I Fundamental of
Bioinformatics 6 4 25 75 100
20 PDBI1C2 Core II Statistics for
Bioinformatics 6 4 25 75 100
20PDBI1C3 Core III Basic Structural Biology
6 4 25 75 100
20PDBI1C4 Core IV Computer Programming 6 4 25 75 100
20PDBI1C5P Core V C Programming and Web
Publishing – Practical 6 4 25 75 100
TOTAL 30 20 125 375 500
II
20PDBI2C1 Core VI Database Management
Systems 6 4 25 75 100
20PDBI2C2 Core VII Genomics and Proteomics 6 4 25 75 100
20PDBI2C3 Core VIII Computational Biology 6 4 25 75 100
20PDBI2C4 Core IX Molecular Modelling and
Drug Design 6 4 25 75 100
20PDBI2C5P Core X Bioinformatics - Practical 6 4 25 75 100
TOTAL 30 20 125 375 500
GRAND TOTAL 60 40 250 750 1000
Post Graduate Diploma in Bioinformatics (P.G.D.B.I)
Programme Specific Outcome
At the end of the programme, students will be able to:
Explain the fundamental principles of Bioinformatics and statistical applications in
bio informatics.
Outline the process of generation, manipulation and representation of molecules for
drug modeling.
Describe the basic structure of biological molecules, process of acquiring the
structures and the interaction between the molecules.
Develop and apply basic computer programming to build biological algorithms and
models to study their relationships.
Deduce the interrelationship between genomics and Proteomics, techniques involved
in analyzing proteomics and its applications.
SEMESTER I: CORE - I FUNDAMENTAL OF BIOINFORMATICS
Subject Code: 20PDBI1C1 Max. Marks 100
Hours / Week: 6 Internal Marks: 25
Credit: 4 External Marks: 75
Unit I: 18 Hours
Bioinformatics – an Overview, Definition – Scope and History of Bioinformatics
Networks – Internet in Bioinformatics, #EMBnet – Commercial Databases and
Software’s, # Intranet and Internet Packages. Role of Bioinformatics.
Unit II 18 Hours
Languages – Basics of C Programming, Array, Structure and Function. Perl – Basics,
String handling. HTML – Basics, Text handling, Image handling, Links and Tables. #XML – Basics, data binding and record sets#.
Unit III 18 Hours
Introduction to Biological database – Protein Information Resources – Biological
Databases, Primary Sequence Databases, Protein Sequence Databases, and Nucleotide
Sequence Database-#Secondary Databases, Metabolic pathway databases#.
Unit IV 18Hours
Genome Information Resources – DNA sequence Databases – EMBL DDBJ, Genbank
GSDB (Genome, Sequence Database), #UniGene-Comprehensive microbial
Resource,#Sequence alignment – local and global alignment.
Unit V 18 Hours
Evolution of Bioinformatics – Scope – Potentials of Bioinformatics, Human Genome
Project – Application of Bioinformatics #Bioinformatics in India – Future of
Bioinformatics#. Cheminformatics – Ayurinformatics.
#-----------#Self-study portion
Text Books:
T.B 1. Attwood T.K and D.J. Parry-Smith, Introduction to Bioinformatics,
PearsonEducation Ltd., New Delhi (2004).
T.B 2 .Arthur M. Lesk, Introduction to Bioinformatics, Oxford University Press,
NewDelhi (2003).
Unit I: Chapter I Section 1, 8-11. T.B - 1
Unit II: Chapter II Section 6- 9. T.B - 2
Unit III: Chapter I Section 1.2, 1.1, 3.2. T.B -3
Unit IV: Chapter VIII Section 180-191 T.B -3
Unit V: Chapter V Section 1-23. T.B - 2
Books for References:
1. Swindell, S.R., R.R.Miller and G.S.A. Myers (Eds.), Internet for the Molecular Biologist,
Horizon Scientific Press, Wymondham, UK, (1996).
2. Andrea Cabibbo, Richard Grant and Manuela Helmer-Citterich (Eds.), The Internet for
Cell and Molecular Biologists (2nd Edn.), Horizon scientific Press, Norwich, UK (2004).
Web reference:
https://www.epictraining.ca/course/15958/biological databases/-distance
https://bioinformatics.mit.edu/
COURSE OUTCOMES:
CO 1: Identify the scope of Computational Biology and Bioinformatics.
CO2. Ability to design programs with interactive Input and Output program c.
CO3.The Study of understanding biological information. Retrieval methods for
DNA sequence.
CO4. Gain the knowledge Major Biological Databases and Information.
CO5. Determine the analyzed molecular biology, clinical medicine and other
disciplines.
Mapping with programme outcomesand programme specific outcomes
PO1 PO2 PO3 PO4 PO5 PSO1 PSO2 PSO3 PSO4 PSO5
CO1 ✓ ✓ ✓ ✓ ✓ ✓ ✓
CO2 ✓ ✓ ✓ ✓ ✓ ✓ ✓
CO3 ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓
CO4 ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓
CO5 ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓
Number of matches (✓) - 44
Mapping Score - 88 %
If number of matches (✓) ≥35 (ie.) 70% and above - - High
Prepared by: Checked by:
1. Mr.K.Gobalan - 1. Dr. A. Khaleel Ahamed.
2. Dr. J. Sebastin Raj
SEMESTER I: CORE II
STATISTICS FOR BIOINFORMATICS
Subject Code: 20PDBI1C2 Max Marks: 100
Hours / Week: 6 Internal Marks: 25 Credit: 4 External Marks: 75
Unit I 18 Hours
Measures of central Tendency – Arithmetic Mean – Median – Mode – Quartiles –Range – #Quartile deviation – Mean deviation#. Quartiles– Calculation of Quartiles – Standard
Deviation.
Unit II 18 Hours
Probability – Frequency Theory of Probability – Limitations – View of Probability –
Addition Theorem – Multiplication Theorem - #Baye’s Theorem and related
problems#.
Unit III 18 Hours
Theoretical Distributions – Binomial, Poisson and Normal – Importance of Normal
Curve # fitting of the Distributions and its properties - Z-score, P-value and E-value#.
Unit IV 18 Hours
Theory of Attributes – Introduction – Dichotomy – Consistency of Data –
Independence of Attributes – Association of Attributes – #Rules coefficient of
Association#.
Unit V 18Hours
Sampling Distributors – Large and small sample tests – Theories of probability,
Student’s t2 test, X2 test, F-test – and chi square test for goodness of fit #. Normal test
and their applications#.
#----------# Self-study portion
Text Books: T.B 1: Gupta S.C and V.K. Kapoor, Fundamentals of Mathematical Statistics, 11th Edition,
Sultan Chand & Sons, New Delhi, 2002.
T.B 2: Pillai R.S.N and V. Bagavathi and S. Chand Statistics (1984). Unit I: Chapters 9 Sections 121 - 129. T.B-1
Unit II: Chapters 18Sections 686-695. T.B-1
Unit III: Chapters 19 Sections 735 - 748 T.B-1
Unit IV: Chapters 5 Sections 35-42.T.B-2
Unit V: Chapters 1 Sections 222-224. T.B-2
Books for Reference:
1. Gupta, S.P., Statistical Methods, Sultan Chand & Sons, 1996.
2. Forthofer, L., Introduction to Biostatistics, Academic Press, 1995.
3. Robert R. Sokal and F.J. Rohlf, Introduction to Biostatistics (Biology- Statistics Series),
W.H. Freeman & Company, New York, 1987.
Web References:
1. https://nptel.ac.in/courses/statistics 102103012/s
COURSE OUTCOMES:
CO1: Determine the category of measures of central tendency, dispersion and correlation
for analysis of data.
CO2: Improve the new concepts of probability and random variables.
CO3: Identify the application some standard distributions and their properties.
CO4: Gain the knowledge about frequency theory of probability and its related problems.
CO5: Intellectual about the rule’s coefficient of association.
Mapping with Programme Outcomes and Programme Specific Outcomes:
PO1 PO2 PO3 PO4 PO5 PSO1 PSO2 PSO3 PSO4 PSO5
CO1 ✓ ✓ ✓
CO2 ✓ ✓ ✓ ✓ ✓ ✓ ✓
CO3 ✓ ✓ ✓ ✓ ✓
CO4 ✓ ✓ ✓ ✓ ✓ ✓ ✓
CO5 ✓ ✓ ✓ ✓ ✓ ✓ ✓
Number of matches (✓) - 34
Mapping Score - 68 %
If number of matches (✓) ≥30 (ie.) 60% and above - Moderate
Prepared by:
1. Mr.Gobalan
Checked by:
1. Dr. A. Khaleel Ahamed.
2. Dr. T. Nargis Begum
Semester I: CORE III
BASIC STRUCTURAL BIOLOGY
Subject Code:20PDBI1C3 Max Marks: 100
Hours / Week: 6 Internal Marks: 25
Credit: 4 External Marks :75
Unit I 18 Hours
Cell Structure and Ultra cell structure of Prokaryotic and Eukaryotic cells – Cell wall – cell
membrane – Biomembranes – Organelles. – Diffusion – #Active and Passive Transport#.
Unit II 18 Hours
Carbohydrates – Classification Types – Structure – Function. Lipids –Classification Types –
Structure – Function.
Unit III 18 Hours
Introduction and Physiochemical Properties of Nucleic Acids – DNA and RNA. Watson and
Crick Model of DNA and the different forms of DNA.RNA structure – Principles and
Prediction. # Gene Structure#.
Unit IV 18 Hours
Classification of amino Acids. Classification and three-Dimensional structure of proteins.
Overview of protein structure – Primary, Secondary, Tertiary and Quaternary
structures.#Ramachandran plot and bonds stabilizing protein structure#.
Unit V 18 Hours
Principles of Structural Organization and Conformational Analysis. Prediction of protein
structure - Modeling homology, Chou and Fasman method. Basic Principles of X-ray
Diffraction Studies, #NMR#, Mass Spectroscopy in Identifying Protein Conformation#.
#.........# Self-study portion
Text Books:
1. Van Holde, Principles of Physical Biochemistry –Prentice Hall. 2006
2. Horst FriebolinWitey, Basic One & Two dimensional NMR sepectroscopy–VCH – 1990.
Books for References:
1. Lechninger, David L. Nelson, Michael M. Cox., Principles of Biochemistry –3rd
Edition Macmillan worth Publishers, 2000.
2. G.E.Shultz and R.H.Schirmer,Principles of Protein structure, Springer –Verlag, New
York. 2002.
Web References:
https://nptel.ac.in/courses/102103012/
Course Outcomes:
CO1 Acquire the basic and fundamental concepts of cell biology.
CO2 Explain the knowledge in basic energy sources.
CO3 Apply the principle, Physiochemical properties, structure of nucleic acids.
CO4 Appraise the basic science of Protein structure including mechanisms.
CO5 Formulate the key experimental processes required to evaluate protein structure,
functions and to apply them to solve biochemical problems.
Mapping withProgramme outcome and Programme Specific Outcome
PO1 PO2 PO3 PO4 PO5 PSO1 PSO2 PSO3 PSO4 PSO5
CO1
CO2
CO3
CO4
CO5
Number of matches (✓) - 34
Mapping Score - 68 %
If number of matches (✓) ≥30 (ie.) 60% and above - Moderate
Prepared by: Checked by: 1. Dr. T. Nargis Begum - 1. Dr. J. Sebastin Raj
2Dr.A. Khaleel Ahamed
SEMESTER I: CORE IV COMPUTER PROGRAMMING
Subject Code: 20PDBI1C4 Max Marks: 100
Hours / Week: 6 Internal Marks: 25
Credit: 4 External Marks: 75
Unit I 18 Hours Block diagram of computer (input and output devices) generation – advantages and
limitations of computers – Basics of operating systems DOS, Windows NT and XP,
UNIX – #Application software’s#.
Unit II 18 Hours
Introduction to internet, service on internet – internet tools, HTML, text formatting –
Adding images – Tables – Frames to web pages. Web services – WWW, URL, DNS –
Servers, WEB servers, Browsers, IP Addressing, Communication Technology –
Networking: LAN, #WAN and MAN, wireless communication#.
Unit III 18 Hours
Identifiers and keywords – Constants, Variables and data types – #Operations and
Expression – Data input and output#.
Unit IV 18 Hours
Control structure – If and Switch statement – While, Do – While and for statements –
Goto statement, #Arrays - 1 D array -2 D array#.
Unit V 18 Hours
Web Publishing Internet – WWW – Designing web site – Basics of creating a web
page with HTML – Linking – Text formatting – #Adding Images and background to
HTML pages – Tables– Image maps#.Function – User defined functions – Defining
and assessing functions – Passing arguments - Functions prototypes – character strings
– string functions – recursion – storage classes – structure – union.
# -----------#Self-study portion
Text Books:
T.B 1: Balagurusamy E., Object Oriented Programming with C++” –– TMH-2000.
T.B.2: Monica D’Souza & Jude D’Souza “Web Publishing” –– TMH– 2001.
Unit I: Chapters III Sections 1-37.T.B-1 Unit II: Chapters II Sections49-210.T.B-1 Unit III: Chapters IV Sections 65-175.T.B-1 Unit IV: Chapters VI Sections 2-59. T.B-2 Unit V: Chapters VII Sections 11-109. T.B-2 Books for Reference:
1. Robert Lafore., Object Oriented Programming in C++ - Galgotia.2000.
2. YeshwantKanetkar., let us C++ -– BPB. 2001
3. Steve Wright., Instant HTML Programmer’s Reference –– WROX Press Ltd.2011.
Web reference:
1. https://ocw.mit.edu/courses/computer program /7-06- -spring-2007.
2. https://ocw.mit.edu/courses/biology/7-06-computer application-spring-2010/
COURSE OUTCOMES:
CO 1: Develop the foundation for higher studies in the field of Computer
Application.
CO 2: Ability to design programs with Interactive Input and Output
CO 3: Gain ability to develop responsive web applications
CO 4: Explore different web extensions and web services standards.
CO 5: Acquire knowledge and skills for creation of web site considering both client and
server-side programming.
Mapping with programme outcomes and programme specific outcomes:
No. of matches 40
Mapping Score 80%
If number of matches ≥35 (i.e.) 70% and above High
Prepared by: Checked by:
1. Mr. K.Gobalan 1. Dr.A.Khaleel Ahamed.
2. Dr. T. Nargis Begum
PO1 PO2 PO3 PO4 PO5 PSO1 PSO2 PSO3 PSO4 PSO5
CO1
CO2
CO3
CO4
CO5
SEMESTER I: CORE V C PROGRAMMING AND WEB PUBLISHING - PRACTICAL
Subject Code:20PDBI 1C5P Max Marks: 100
Hours / Week: 6 Internal Marks: 25
Credit: 4 External Marks : 75
1. Factorial of a given number.
2. Sorting and merging two arrays of numbers.
3. Sorting names in alphabetical order.
4. Reversing a given string.
5. Checking for palindrome.
6. String Manipulation – String copy, String length, String concatenation, String
comparisonand String reverse. 7. Mean, median, mode and standard deviation calculations.
8. Storing and retrieving amino acid sequences using structure data types.
9. Swapping two values using pointers.
10. File Processing – Creation and simple processing.
11. Computing amino acid composition of a given protein sequence.
12. Enumerate RNA Secondary Structure.
Web Publishing:
1. Create a web page for your University / College using HTML. The opening page
shouldprovide hyperlinks to other pages (add animation and sound effects
appropriately).
2. Creating a web page to get protein sequence data and compute and display amino
acid composition.
3. Creating a web page to get nucleic acid sequence data and compute and display
base composition.
Text Books:
1:E. Balagurusamy. Object Oriented Programming C++. Third Edition 2006.
2:A. Jitender. Introduction to HTML.“Web Publishing” – Monica D’Souza & Jude
D’Souza – TMH– 2001. Third Edition 2008.
Books for References:
1. Gary J. Bronson (A First Book of ANSI C Third Edition 2001).
2. Jitender Kumar Chakra, Programming with C and C++. (Second Edition 2006).
3. Yes want Kantar. let us C++ – BPB. (2000)
4. Steve Wright., Instant HTML Programmer’s Reference –– WROX Press Ltd.
2011.
Web reference:
1. https://www.youtube.com/watch?v=c program/k1pp
2. https://www.youtube.com/watch?v=html /k1O9jBHgsxs
COURSE OUTCOMES:
CO1: Describe the C programming concepts like Structures, Pointers and Command line
arguments and data structures
CO2: Identify the application of some basic programs in C and Web based application.
CO3: Acquire the knowledge Practice the use of conditional and looping statements.
CO4: Illustrate the structure; implement arrays, functions and pointers.
CO5: Improve the new skills to handle strings and files.
Mapping with programme outcomes and programme specific outcomes:
PO1 PO2 PO3 PO4 PO5 PSO1 PSO2 PSO3 PSO4 PSO5
CO1
CO2
CO3
CO4
CO5
No. of matches 40
Mapping Score 80%
If number of matches ≥35 (i.e.) 70% and above High
Prepared by:
1. Mr.K.Gobalan
Checked by:
1. Dr.A.KhaleelAhamed
2. Dr. Y. Arsia Tarnam
Semester II: CORE VI
DATABASE MANAGEMENT SYSTEMS
Subject Code:20PDBI 2C1 Max Marks: 100
Hours / Week: 6 Internal Marks: 25
Credit: 4 External Marks :75
Unit I 18 Hours
Data base: Introduction – Basic Technology and Data Basics – #Objective of a Data base
organization – Entities & Attributes #.
Unit II 18 Hours Data Models: Introduction – Schemes & Sub Schemes – Data base Management Systems – File
Database – Tree Structures. # Relational Databases – Normal Forms #.
Unit III 18 Hours Data Base Languages: Introduction – Data Description Languages – the CODASYL Data
Description Language – #Query Languages – Data Dictionaries #.
Unit IV 18 Hours Physical Organization: Introduction – Criteria affecting physical organization –Differences
between physical & logical organization – #Addressing Techniques –Index sequential
organization – Hashing #.
Unit V 18 Hours Database security: Data Classification– Database access Control – Types of Privileges –
Cryptography- Statistical Databases- Distributed Databases- Processing. #Object Oriented
Databases-XML Databases#.
#..................# Self-study portion
Text Book:
T.B. 1. James Martin, Computer Database Organization, Prentice Hall of India, 2016
Books for Reference:
1. James Martin, Principles of Database Management, Prentice Hall of India, 2012
2. C.J. Date, An Introduction to Database systems, 3rd edition, Narosa Publishing House,
2004
Web References:
https://nptel.ac.in/courses/106105175/
Course outcomes
CO1 Acquire the basics, concepts, objectives of Database.
CO2 Describe the fundamental elements of data models and database management systems.
CO3 Apply and use data manipulation language to query update and manage a data base.
CO4 Analyze the physical and logic database designs and addressing techniques: indexing methods and
Hashing.
CO5 Construct a simple database system with the understanding of essential DBMS concepts
such as Database security.
Mapping withProgramme outcome and Programme Specific Outcome
PO1 PO2 PO3 PO4 PO5 PSO1 PSO2 PSO3 PSO4 PSO5
CO1
CO2
CO3
CO4
CO5
If number of matches () ≥ 30 (ie.) 60% and above –Moderate
Prepared by: Checked by: 1. Dr. T. Nargis Begum - 1. Dr. J. Sebastin Raj
2. Dr. A. Khaleel Ahamed
*****
SEMSTER II: CORE VII
GENOMICS AND PROTEOMICS
Subject Code:20PDBI 2C2 Max Marks: 100
Hours / Week: 6 Internal Marks: 25
Credit: 4 External Marks: 75
Unit I 18
Hours
The genetic material – Identification of genetic material, genetic code, concept of gene – operon
concept – lac and trp operons, #promoters and repressors.
Unit II 18
Hours
Different types of genome maps and their uses, genetic and physical mapping techniques –
Genomics – definitions – pharmacogenomics – taxicogenomics – #prokaryotic and eukaryotic
genome – genome relationships – human genomics.
Unit III 18
Hours
Genomics Whole genome analysis – Physical methods of sequencing – automated sequencing –
genome expression and analysis – serial analysis. #code micro assay and microchips.
Unit IV 18
Hours
Proteomics Definition – Transcriptomics; Proteomics, metabolomics. Techniques of proteomics
– 2D PAGE, Multidimensional protein identification (Mud PIT) Isotopically coded affinity Tag
(ICAT), Mass spectrophotometer – (MALDI – TOF) MS. #Application of functional genomics in
basic biology, target / marker identification, target toxicology, microbial drug,tumour
immunology, vaccine discovery, drug design.
Unit V 18
Hours
Proteome and technology – Primary attributes for protein identification – protein super families.
A brief account of genetic engineering –Vectors used in genetic engineering-Genomic DNA
library-Cloning and modification methods-#Site Directed mutagenesis-Commercial applications.
#..............# Self-study portion
Text Books:
T.B. 1. Baxevanis AD and B.F.F. Ouellette, Wiley Bioinformatics – A practical guide to the
analysis of genes and proteins. (ed) – Interscience, New York, 2001.
T.B. 2. Doolittle RF Molecular evolution, Computer Analysis of Protein and Nucleic acid
Sequences, Methods in Enzymology, Academic Press, New York. 1990.
Books for References:
1. K. Faber. Biotransformation in Organic Chemistry, Springer Verlag. 1992.
2. P.Gerbardt, R. G.Murray, W. A.Wood, N. R.Kreig. Methods for General and Molecular
Bacteriology – American Society for Microbiology Washington D.C., 1994.
Web Reference:
1.https://courses.lumenlearning.com/boundless-biology/chapter/genomics-and-proteomics/
2. https://www.ncbi.nlm.nih.gov/books/NBK19861/
Course Outcomes:
On completion of this course, the student will be able to:
CO1. Infer the basic concepts of genomics, transcriptomics and proteomics.
CO2. List and discuss the use of genomics and proteomics in human health.
CO3. Suggest and outline solution to theoretical and experimental problems in Genomics and
Proteomics fields.
CO4. Helpful to those students who want to work in core facilities and commercial biological
and medical laboratories as well as in their postgraduate studies.
CO5. Deals with a rapidly evolving scientific area that introduces students into genomes,
proteomes
and databases that store various data about genes, proteins, genomes and proteomes.
Mapping with Programme Outcomes and Programme Specific Outcomes.
No of matches 36
Mapping Score 72%
If number of matches ≥ 35 (ie) 70% and above High
Prepared by: Checked by:
1.H.F.Seyed Mafiya Haniff 1.Dr.A.Nishanthini
2. Dr.A.Khaleel
Ahamed
SEMSTER II: CORE VIII
COMPUTATIONAL BIOLOGY
Subject Code:17PDBI2C3 Max Marks: 100
Hours / Week: 6 Internal Marks: 25
Credit: 4 External Marks :75
Unit I 18
Hours
Structure of DNA & Protein – Sequence analysis – pairwise sequence comparison – sequence
queries against biological databases – BLAST and FASTA – #multifunctional tools for analysis#.
Unit II 18
Hours
Multiple sequence alignments, Phylogenetic alignment – profiles and motifs – distance and
similarity – #evolutionary basis of sequence alignment – scores and gaps#.
PO1 PO2 PO3 PO4 PO5 PSO1 PSO2 PSO3 PSO4 PSO5
CO1 ✔ ✔ ✔ ✔ ✔
CO2 ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔
CO3 ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔
CO4 ✔ ✔ ✔ ✔ ✔ ✔ ✔
CO5 ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔
Unit III 18
Hours
Protein structure visualization – tools structure – classification, alignment and analysis. Solvent
accessibility and Interactions – Physico-chemical properties, structure optimization. #Protein
resource databases#.
Unit IV 18
Hours
Predicting Protein structure and function from sequence – Determination of structure – feature
detection – secondary structure prediction – Predicting 3 D structure. #Protein modeling#.
Unit V 18
Hours
Genomics and Proteomics – Sequencing genomes – sequence assembly – genome on the web –
annotating and analyzing genome sequences. #Proteomics – biochemical pathway databases –
submitting sequence to the databases#.
#..................# Self-study portion
Text Books:
T.B-1 A.D.Baxevanis, B.F.F. Ouellette Bioinformatics: A practical guide to the analysis of
genes and proteins– Wiley Interscience – New York, 2001.
T.B-2 StephenMisener& Stephen A. Krawetz, Bioinformatics: Methods and Protocols
HumanaPress, New Jersey, 2000.
Unit I Chapters III Sections 3-21.T.B-1
Unit II Chapters III Sections 20.3-4.21.T.B-1
Unit III Chapters III Sections 22-55.T.B-1
Unit IV Chapters V Sections 5.1-5.6.T.B-2
Unit V Chapters VII Sections 151-166.T.B-2
Books for Reference:
1. Des Higgins & Willie Taylor, Bioinformatics: Sequence, structure and databanks – Oxford
University Press, 2000.
Course Outcomes:
On the completion of the course, students will be able to:
CO 1. Describe different types of biological database and sequence submission tools.
CO 2. Summarize the basics of sequence alignment and various approaches in phylogenetic
analysis.
CO 3. Assess the structure, properties and interactions of protein and its databases.
CO 4. Explain the structure and various approaches in 3D structure prediction.
CO 5. Classify and explain the tools and algorithms used for genome sequencing assembly.
Mapping with Programme Outcomes and Programme Specific Outcomes
PO1 PO2 PO3 PO4 PO5 PSO1 PSO2 PSO3 PSO4 PSO5
CO1 ✔ ✔ ✔ ✔ ✔ ✔
CO2 ✔ ✔ ✔ ✔ ✔ ✔
CO3 ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔
CO4 ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔
CO5 ✔ ✔ ✔ ✔ ✔ ✔
Number of matches (✓) - 36
Mapping Score - 72 %
If number of matches (✓) ≥35 (ie.) 70% and above - High
Prepared by: Checked by:
1.Dr. Y. ArsiaTarnam 1. Dr. J. Sebastinraj
2. Dr. A. Khaleel Ahmed
SEMSTER II: CORE IX
MOLECULAR MODELING AND DRUG DESIGN
Subject Code:17PDBI2C4 Max Marks: 100
Hrs / Week: 6 Internal Marks: 25
Credit: 4 External Marks :75
Unit I 18 Hours
Recent advances in drug design methodologies, bimolecular structure, Structure activity
relationship, #Pharmacokinetics, #structure-based drug design#.
Unit II 18 Hours
Molecular basis of drug action, Pharmacophoric pattern, ADME Properties, quantitative
structure activity relationship, #Use of genetic algorithms and principle component analysis in
the QSAR equations#.
Unit III 18 Hours
Molecular modeling, quantum mechanical and molecular orbital methods, introduction to semi-
empirical, molecular mechanics and abintio techniques.Simulation techniques, potential energy
surfaces, docking and modeling substrate – receptor interactions#.
Unit IV 18 Hours
Historic development of drug discovery, Modern drug discovery Software tools for modeling
bio-molecules. #Molecular electrostatic potentials, charge analyses. Protein conformations,
folding and mutation through modeling#.
Unit V 18 Hours
Use of Genomics and Proteomics for understanding diseases at molecular level strategies for
target identification and #lead design#.
#.................# Self-study portion
Text Books:
T.B-1 Andrew Leach, Molecular Modelling: Principles and Applications, 2nd Edition, Addison
Wesley Longman, Essex, England, 1996.
T.B-2 Alan Hinchliffe, Molecular Modelling for Beginners, John-Wiley, 2003.
Unit I Chapters XI Sections 12.1.T.B-1
Unit II Chapters X Sections 10.1-10.9.T.B-2
Unit III Chapters VIII Sections 8.1-8.9.T.B-2
Unit IV Chapters VII Sections 7.1-79.T.B.1
Unit V Chapters I Sections 1.1-1.10.T.B-1
Books for Reference:
1. N. Cohen (Ed.), Guide Book on Molecular Modeling in Drug Design, Academic Press, San
Diego, 1996.
Course Outcomes:
On the completion of the course students will be able to:
CO 1. Discuss various techniques and concepts used in structure-based drug design.
CO 2. Describe the algorithms used in drug analysis.
CO 3. Analyze the principles involved in molecular modeling and drug design.
CO 4. Demonstrate the various tools employed in drug discovery and its applications.
CO 5. Systematize about genomics and proteomics in disease analysis at molecular level.
Mapping with Programme Outcomes and Programme Specific Outcomes
PO1 PO2 PO3 PO4 PO5 PSO1 PSO2 PSO3 PSO4 PSO5
CO1 ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔
CO2 ✔ ✔ ✔ ✔ ✔ ✔
CO3 ✔ ✔ ✔ ✔ ✔ ✔
CO4 ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔
CO5 ✔ ✔ ✔ ✔ ✔ ✔
Number of matches (✓) - 34
Mapping Score - 68 %
If number of matches (✓) ≥30 (ie.) 60% and above - Moderate
Prepared by: Checked by:
1. Dr. Y. ArsiaTarnam 1. Dr. J. Sebastinraj
2. Dr. A. Khaleel Ahmed
SEMESTER II: CORE X
BIOINFORMATICS – PRACTICAL
Subject Code:17PDBI2C5P Max Marks: 100
Hrs / Week: 6 Internal Marks: 25
Credit: 4 External Marks :75
1. Multiple alignments- using CLUSTAL W
2. Phylogenetic Analysis using NJ plot.
3. BLAST, FASTA programs for sequence database search.
4. Small molecule building using che1nDraw or chem. Sketch.
5. Evaluation of protein structure by Swiss PDB viewer and by other molecular visualization
tools.
6. Calculation of phi – psi angles - Ramachandran plot.
7. Homology modeling of a given protein sequence.
8. Small molecule building using chemSketch.
9. Metabolic pathway prediction
10. Docking Using Patch Dock.
Text Books:
T.B-1 D. Andreas, B.F. Baxevanis, Francis Ouellette, Bioinformatics- A Practical Guide to the
Analysis of Genes and Proteins, Wiley-Interscience, 3rd edition, 2006.
T.B-2 A. Baxevanis and B.F. Ouellette, Bioinformatics: A practical Guide to the Analysis of
Genes and Proteins, Wiley-Inter science, Hoboken, NJ, 1998.
Books for References:
1. S.C. Rastogi, Namita Mendiratta Parag Rastogi. Bioinformatics Concepts, Skills &
Applications, CBS Publishers & Distributors, First edition, 2003.
2. K. Teresa, Attwood and J. David, Parry Smith, Introduction to Bioinformatics,
Pearson Education, 1999.
Course Outcomes:
On the completion of the course students will be able to:
CO 1. Describe about sequencing alignment and similar search tool
CO 2. Provide hands on training on various tools and techniques employed in biological
sequence analysis.
CO 3. Explain about protein structural analysis using Bioinformatics tools.
CO 4. Expose to several DNA and protein databases.
CO 5. Practice methods and tools used for phylogenetic analysis.
Mapping with Programme Outcomes and Programme Specific Outcomes:
PO1 PO2 PO3 PO4 PO5 PSO1 PSO2 PSO3 PSO4 PSO5
CO1 ✔ ✔ ✓ ✔ ✔ ✔ ✔ ✔
CO2 ✔ ✔ ✔ ✔ ✔ ✔
CO3 ✔ ✔ ✔ ✔ ✔ ✔
CO4 ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔
CO5 ✔ ✔ ✔ ✔ ✔ ✔
Number of matches (✓) - 34
Mapping Score - 68 %
If number of matches (✓) ≥30 (ie.) 60% and above - Moderate
Prepared by: Checked by:
1. Dr. Y. ArsiaTarnam 1. Dr. J. Sebastinraj
2. Dr. A. Khaleel Ahmed
******